Showing : voom • reset
6
votes
5
replies
672
views
How do I fix an odd voom plot in a combined dataset?
limma Normalization voom
updated 10 weeks ago by 68k • written 11 weeks ago by • 0
0
votes
2
replies
568
views
sva: get a sv for RIN scores
limma sva variancePartition voom RNASeq
updated 3 months ago by 52k • written 3 months ago by ▴ 10
1
vote
8
replies
1.6k
views
Combining RNAseq and microarray data using edgeR/limma-voom
limma voom RNASeq edgeR Microarray
written 4 months ago by • 0
2
votes
4
replies
810
views
how limma work with continous variables
GordonSmyth limmaGUI lmFit voom
updated 7 months ago by 52k • written 7 months ago by ▴ 40
4
votes
4
replies
1.3k
views
Using both voom and removeBatchEffect, will they double adjust the data or is it the right way to perform this
limma adjustment voom removeBatchEffect covariates
8 months ago sukeshinik5 ▴ 20
1
vote
2
replies
776
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
10 months ago Dylan.Sheerin • 0
0
votes
2
replies
551
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 11 months ago by • 0
0
votes
2
replies
603
views
voom(calcNormFactors()) for normalization of RNAseq counts for WGCNA
Voom Limma WGCNA
11 months ago Gimena • 0
5
votes
2
replies
1.2k
views
Filter genes by expression for voomLmFit
DEG edgeR limma voom filterByExpr
updated 15 months ago by 52k • written 15 months ago by • 0
11
votes
3
replies
2.5k
views
limma::voom vs edgeR::voomLmFit - when to use?
edgeR limma voom RNASeq muscat
written 15 months ago by • 0
3
votes
4
replies
1.1k
views
Is it appropriate to apply linear mixed models to Voom transformed data?
stats r RNASeqData limma voom
16 months ago pl23 • 0
2
votes
4
replies
1.1k
views
limma + voom combine voomWithQualityWeights and duplicateCorrelation
voom RNASeq limma
16 months ago Tyler Sagendorf ▴ 10
5
votes
3
replies
1.0k
views
limma: More differentially expressed genes when factor included in model than when used as blocking factor
voom blocking limma
updated 17 months ago by 52k • written 17 months ago by ▴ 180
1
vote
6
replies
3.3k
views
Can I use EdgeR log2(cpm) instead of voom log2(cpm) to be analyzed as microarray data?
limma edger timecourse without replicate voom
written 8.3 years ago by ▴ 10
1
vote
1
reply
1.8k
views
How to do GSEA over limma + voom DGE ?
GSEA voom limma
updated 20 months ago by 52k • written 20 months ago by • 0
1
vote
5
replies
1.6k
views
Does voom normalization quantile create difference in DGE genes when distribution of patients is similar (no big differences in quantiles)?
limmaGUI normalization limma voom Normalization
updated 20 months ago by 52k • written 20 months ago by • 0
0
votes
1
reply
734
views
How to do PFS after Voom + Limma DGE ?
RNASeqData limma voom PFS DGE
updated 21 months ago by 68k • written 21 months ago by • 0
0
votes
1
reply
885
views
Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 23 months ago by 52k • written 23 months ago by • 0
3
votes
4
replies
1.8k
views
Processing data with voom "expression values" and "weights"
limma voom
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
1
vote
1
reply
803
views
Alternatives to Voom in experiments without replicate
limma edgeR Voom
updated 2.2 years ago by 52k • written 2.2 years ago by • 0
1
vote
3
replies
1.5k
views
diagnosing shifted MD plots/biased DEGs despite filtering
edgeR voom normalization DifferentialExpression
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
1
vote
1
reply
1.1k
views
Voom variance values: Some minor confusion about which variance is fed to lowess when using a design matrix of covariates
voom
updated 2.3 years ago by 52k • written 2.3 years ago by • 0
1
vote
10
replies
3.2k
views
multiple voom runs with duplicateCorrelation and negative values in limma
limma voom
2.6 years ago • updated 2.5 years ago Hilary ▴ 40
2
votes
2
replies
1.6k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.7 years ago Yang Shi ▴ 10
2
votes
4
replies
1.8k
views
pre-ranked GSEA or not?
log2FC DESeq2 GSEA voom limma
updated 2.7 years ago by 52k • written 2.7 years ago by ▴ 10
5
votes
6
replies
2.3k
views
Removing the duplicated genes before limma::voom by using limma::avereps
RSEM avereps voom limma RNASeq
2.7 years ago Yang Shi ▴ 10
2
votes
4
replies
2.3k
views
Doing normalization when using voom for DEG analysis?
limma RSEM voom Normalization
2.7 years ago Yang Shi ▴ 10
2
votes
9
replies
3.4k
views
Stuck on how to voom-limma on RSEM data from TCGA
TCGA r RNASeqData voom limma
2.8 years ago • updated 2.7 years ago Peipei • 0
2
votes
2
replies
2.3k
views
Handling NA values in limma's voom design matrix
limma voom design NAs
updated 2.8 years ago by 52k • written 2.8 years ago by ▴ 10
2
votes
4
replies
4.3k
views
Limma: How to deal with multiple batch effects and what is going on under the hood
limma voom
updated 2.9 years ago by 52k • written 2.9 years ago by ▴ 20
0
votes
3
replies
1.9k
views
limma voom contrasts
contrasts limma voom
updated 3.0 years ago by 52k • written 3.0 years ago by ▴ 90
0
votes
3
replies
1.3k
views
Need help with a contrast design for limma with a missing group?
limma VOOM
updated 3.1 years ago by 52k • written 3.1 years ago by ▴ 50
3
votes
5
replies
3.3k
views
limma-trend and voom results do not agree
limma limma-trend voom RNASeq
3.3 years ago Tyler Sagendorf ▴ 10
3
votes
2
replies
2.0k
views
Multi-level design RRBS analysis with voomLmFit
edgeR voomLmFit limma duplicateCorrelation voom
updated 4 months ago by 52k • written 3.3 years ago by • 0
0
votes
2
replies
2.8k
views
Mean-variance trend and identifying significant DE with large amount of biological change in expression in time-series data
voom
3.4 years ago • updated 3.3 years ago hmviit • 0
0
votes
2
replies
1.7k
views
voom flips the sign relative to log(cpm)
limma limma-voom rnaseq voom
updated 3.5 years ago by 52k • written 3.5 years ago by • 0
0
votes
1
reply
2.7k
views
limma/voom for protein intensity data
limma proteomics voom
updated 3.5 years ago by ★ 4.7k • written 3.5 years ago by ▴ 70
0
votes
2
replies
1.2k
views
limma voom; fitted lines, factors that aren't of interest, and hypothesis testing
topTable voom contrasts
3.6 years ago James • 0
0
votes
2
replies
1.2k
views
voom-limma workflow for RNAseq samples with very different numbers of counts
voom limma RNASeq
4.0 years ago annadv • 0
0
votes
2
replies
7.3k
views
TPM data in limma/voom
voom limma DifferentialExpression edgeR
4.1 years ago RJM • 0
1
vote
1
reply
1.8k
views
Limma-Voom - Time series experiment with one group (duplicateCorrelation() function)
voom duplicateCorrelation() timeseries limma
updated 4.2 years ago by 52k • written 4.2 years ago by ▴ 10
6
votes
13
replies
7.0k
views
How to use RSEM value to find differentially expressed genes
RSEM limma edgeR voom normalization
updated 2.7 years ago by 52k • written 4.6 years ago by ▴ 60
0
votes
5
replies
1.7k
views
isoform data, deep sequencing and voom
isoform deep sequencing voom
updated 4.6 years ago by 52k • written 4.6 years ago by ▴ 620
0
votes
4
replies
1.4k
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport isoform voom
updated 4.7 years ago by 52k • written 4.7 years ago by ▴ 620
1
vote
4
replies
1.9k
views
How to compare a single RNA-Seq sample with microarray samples?
voom rna-seq microarray
updated 4.8 years ago by 68k • written 4.8 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Coefficients not estimable voom Lima with multiple numeric covariate
r limma design rnaseq voom
updated 4.8 years ago by 52k • written 4.8 years ago by • 0
4
votes
6
replies
4.2k
views
linear mixed models using edgeR+limma
linear mixed model edger limma voom RNA-seq
updated 4.8 years ago by 52k • written 4.8 years ago by ▴ 10
1
vote
5
replies
2.2k
views
Limma for proteomic data! Please Help!
limma voom lmfit ebayesfit
updated 4.9 years ago by 52k • written 4.9 years ago by • 0
0
votes
2
replies
874
views
estimating variability in absence of replicates for edgeR
edgeR RNAseq voom variability estimator
updated 5.0 years ago by 52k • written 5.0 years ago by • 0
3
votes
6
replies
2.4k
views
paired and unpaired test at the same time with voom limma
limma voom rna-seq paired test unpaired test
updated 5.0 years ago by 52k • written 5.0 years ago by • 0
50 results • Page 1 of 1
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Comment: DESEQ2 looking at main effects while controlling for a continuous variable by Lennie • 0
Thank you so much for taking the time and for the detailed explanation! I was wondering, in your numeric contrast of c(1, -1, 0,0,0), doe…
Answer: DESEQ2 looking at main effects while controlling for a continuous variable by James W. MacDonald 68k
If you use a factor effects model (with an intercept), then you will have a baseline group (the intercept), and all other coefficients exce…
Comment: Issue with DECIPHER::IdTaxa by Daniel • 0
The issue is still there and it is a real pain. ape and ade4 are used by packages like Phyloseq. There should be a way to avoid these inc…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Gordon Smyth 52k
I generally recommend `block=individual` for unbalanced designs, to recover information from incomplete blocks. I would only be disuaded fr…
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with by Devin ▴ 10
Thank you, Gordon, for your responses to all of my questions. For analysis A), in the case when a patient has either a missing timepoint or…
Votes
Answer: DESEQ2 looking at main effects while controlling for a continuous variable
Use of clusterProfiler : Error in testForValidKeytype(x, keytype)
Comment: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
Answer: Using edgeR::voomLmFit for the analysis of paired clinical RNA-seq samples with
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